Mercurial > repos > iuc > hyphy_meme

annotate hyphy_meme.xml @ 12:b69685ed772e draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2413d0043c5d263ecfa75ec0f8614e322fb65f99"
author iuc
date Fri, 08 May 2020 19:11:14 -0400
parents 3d1f153e2aa1
children 5b380f4dbf1c
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1 <?xml version="1.0"?>
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2 <tool id="hyphy_meme" name="HyPhy-MEME" version="@VERSION@+galaxy0">
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3 <description>Mixed Effects Model of Evolution</description>
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4 <macros>
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5 <import>macros.xml</import>
7b3f9c78cf6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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6 </macros>
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7 <expand macro="requirements"/>
7b3f9c78cf6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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8 <command detect_errors="exit_code"><![CDATA[
7b3f9c78cf6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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9 ln -s '$input_file' meme_input.fa &&
7b3f9c78cf6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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10 ln -s '$input_nhx' meme_input.nhx &&
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11 @HYPHYMPI@ meme
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12 --alignment ./meme_input.fa
7b3f9c78cf6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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13 --tree ./meme_input.nhx
7b3f9c78cf6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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14 --code '$gencodeid'
7b3f9c78cf6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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15 --branches '$branches'
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16 --pvalue '$p_value'
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17 --output '$meme_output'
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18 > '$meme_log'
8
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19 ;
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20 @CATCH_MPIERR@
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21 ]]></command>
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22 <inputs>
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23 <expand macro="inputs"/>
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24 <expand macro="gencode"/>
7b3f9c78cf6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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25 <expand macro="branches"/>
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26 <param name="p_value" type="float" value=".1" min="0" max="1" label="P-value threshold"/>
7b3f9c78cf6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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27 </inputs>
7b3f9c78cf6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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28 <outputs>
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29 <data name="meme_log" format="txt"/>
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30 <data name="meme_output" format="hyphy_results.json" />
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31 </outputs>
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32 <tests>
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33 <test>
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34 <param name="input_file" ftype="fasta" value="meme-in1.fa"/>
7b3f9c78cf6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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35 <param name="input_nhx" ftype="nhx" value="meme-in1.nhx"/>
7b3f9c78cf6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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36 <param name="branches" value="All"/>
7b3f9c78cf6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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37 <param name="p_value" value="0.1"/>
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38 <output name="meme_output" file="meme-out1.json" compare="sim_size" delta="25000"/>
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39 </test>
7b3f9c78cf6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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40 </tests>
7b3f9c78cf6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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41 <help><![CDATA[
5
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42 MEME: Mixed Effects Model of Evolution
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43 ======================================
8
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44
5
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45 What question does this method answer?
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46 --------------------------------------
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47
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48 Which site(s) in a gene are subject to pervasive or *episodic*, i.e. only on a
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49 single lineage or subset of lineages, diversifying selection?
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50
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51 Recommended Applications
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52 ------------------------
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53
8
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54 The phenomenon of pervasive selection is generally most prevalent in pathogen evolution and any biological system influenced by evolutionary arms race dynamics
3d1f153e2aa1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 751182d5067ac8378199058d9152ebfcaeb4c4b5"
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55 (or balancing selection), including adaptive immune escape by viruses.
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56 MEME is ideally suited to identify sites under positive selection which
5
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57 represent candidate sites subject to strong selective pressures across the entire phylogeny or only on parts of the phylogeny.
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58
8
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59 MEME is the sole method in HyPhy for detecting selection at individual sites that considers both pervasive and episodic selection.
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60 MEME is therefore our recommended method if maximum power is desired.
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61
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62
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63 Brief description
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64 -----------------
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65
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66 MEME (Mixed Effects Model of Evolution) estimates a site-wise synonymous
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67 (alpha) and a two-category mixture of non-synonymous (beta-, with
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68 proportion p-, and beta+ with proportion [1-p-]) rates, and uses a
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69 likelihood ratio test to determine if beta+ > &alpha; at a site. The
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70 estimates aggregate information over a proportion of branches at a site,
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71 so the signal is derived from episodic diversification, which is a
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72 combination of strength of selection [effect size] and the proportion of
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73 the tree affected. A subset of branches can be selected for testing as
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74 well, in which case an additional (nuisance) parameter will be inferred
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75 -- the non-synonymous rate on branches NOT selected for testing.
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76
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77 Input
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78 -----
1
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79
5
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80 1. A *FASTA* sequence alignment.
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81 2. A phylogenetic tree in the *Newick* format
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82
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83 Note: the names of sequences in the alignment must match the names of the sequences in the tree.
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84
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85
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86 Output
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87 ------
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88
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89 A JSON file with analysis results (http://hyphy.org/resources/json-fields.pdf).
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90
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91 A custom visualization module for viewing these results is available (see http://vision.hyphy.org/MEME for an example)
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92
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93 Further reading
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94 ---------------
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95
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96 http://hyphy.org/methods/selection-methods/#MEME
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97
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98
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99 Tool options
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100 ------------
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101 ::
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102
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103
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104 --code Which genetic code to use
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105
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106 --branches Which branches should be tested for selection?
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107 All [default] : test all branches
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108
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109 Internal : test only internal branches (suitable for
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110 intra-host pathogen evolution for example, where terminal branches
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111 may contain polymorphism data)
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112
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113 Leaves: test only terminal (leaf) branches
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114
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115 Unlabeled: if the Newick string is labeled using the {} notation,
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116 test only branches without explicit labels
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117 (see http://hyphy.org/tutorials/phylotree/)
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118
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119 --pvalue The significance level used to determine significance
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120
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121
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122 ]]></help>
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123 <expand macro="citations">
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124 <citation type="doi">10.1371/journal.pgen.1002764</citation>
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125 </expand>
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126 </tool>